Enhanced Bibliplug [plugin] for WordPress

Description:

Bibliplug was first developed at the Virtual Knowledge Studio in 2009, and is still in use on some dozen project-related Web sites. At the time of development, the goal was to create a central repository for all researchers affiliated with the Studio to organize their academic work. The initial design included: (a) database schema for storing bibliographical references, (b) administration pages to manage the references, and (c) short code for easy retrieval of references based on author, year, and publication type.

In this project we further developed the plugin and re-released it (locally) as Enhanced Bibliplug. Added functionality includes: (a) the ability to connect and synchronize with Zotero accounts (see below), (b) a custom Author page template to display user’s academic title, affiliation, bio, and CV content such as publications and presentations, (c) the ability to export bibliography data in RDF format based on the SPAR ontologies, and (d) the ability to group references based on categories and tags.

(6) publication and presentation reference lists are managed through the Zotero Link, and are associated with registered users. in this way, authors manage their publication lists in Zotero and the resulting lists are automatically appended to the respective author profile pages. (Short codes are used to display a reference list at the bottom of a text.)

Screenshot: Zotero API/Settings (Zotero website)

(7) Publication titles are linked to the source document by entering the URL in the Zotero ‘URL field’

(8) Reference lists are created and managed using a registered (free) Zotero account (individual or group)

(9) references can then be organized is sub-folders, or collections, that are can be individually linked to a WordPress user profile or any WordPress page or post.

(10) the plugin uses the Zotero API to synchronize references with a custom table developed and managed within WordPress database. These settings are available in the Zotero settings at the Feeds/API tab.

Installation:

Upload the Enhanced Bibliplug plugin to your CMS.

Activate it.

To use customized author template, copy

wp_content\plugins\bibliplug\template\author.php

to your theme folder.

If you are using thesis 1.8 for your theme, please copy the content of wp_content\plugins\bibliplug\template\author-loop.php to wp_content\themes\thesis_18\custom\custom_functions.php

If you are using thesis_custom_loop in your custom_functions.php already, just copy the function author(){ ... } to your thesis_custom_loop class.

You’re done!

To upgrade:
In most cases, reinstall the plugin is sufficient.

However, if you upgrading [Version 0.2.5], please go to the option panel in the admin page, under bibliplug, click “Upgrade Schema” for a manual upgrade.

Settings

References can be displayed on any post/page using shortcode bibliplug. For example, to list all John Smith’s journal articles published in 2008, use

You can mix-match any arguments except:
a. If id is used, other arguments are ignored.
b. If category is used, tag is ignored.

Other than types shown in the drop down box when editing a reference, there are two super types you can use.
a. Publication => any type that’s not presentation or conference paper.
b. Presentation => presentation and conference paper.

(2) ensure either ‘author’ or ‘editor’ role is selected (eg. admin role dose not appear in contributor lists)

(3) add middle name/initial and/or (last name) prefix to synchronize with Zotero collections. List by author requires that names are identical here and in Zotero collections. NOTE: the prefix is for last name prefixes, such as ‘van’ or ‘de’ (eg Dutch names)–however, this must be consistent with Zotero naming convention for proper synchronization.

(4) email address and website addresses will be linked to the words [email | website] in your profile, rather than displaying actual addresses. this is an effort to thwart spam robots.

(5) add title, affiliation, and institution on separate lines

(6) bio text can be edited using the rich text editor or via html (same as WP posts and pages).

Feature request: It would be really nice if you could add another attribute to the shortcode so that you could choose to output the reference list in an unordered list (or an ordered list, for that matter).

Hi people. First of all, thanks for this wonderful plugin; it seems to be the only one capable of keeping a proper database of scholarly articles linked to a nice, profiled author database.
On installing this plugin, I noticed that just by activating it, it had already added a couple of journal references on its own, possibly by reading the info embedded into the PDF files in my media library. (Very impressive!)

Problem is, when I try to manually add some more references, I get the following error text at the top of the page:

Curiously, I have an offline version of the blog (running on an offline server with WordPress installed locally on my computer) and I can add new references there. The error happens only on the online version.

In addition, some of the shortcodes don’t work — in neither versions!

Additional info: I’m using WordPress 3.4.2 and the latest version of the plugin (1.3.8).

Hi SomniumLucidus,
Thanks for the feedback. I need additional information to further troubleshoot.

- Which version/engine is your MySQL?
- Go to the settings->bibliplug, and turn on debug option. With debugging on, try it again and email the errors/warnings (if any).
- VERY STRANGE that a couple articles appeared in the db. do you recall the titles?

If none of the above helps, would be be possible to look at your MySQL?

I’ve looked at the plugin again, and for the life of me, I can’t figure out this simple problem: only “administrators” can see the references, edit them or add them. “Editors” or other roles can’t edit.

I’m using the latest wordpress (3.4.1) and the latest bibliplug (1.3.5). Is there something wrong with my setup, or is the plugin broken??

Hello,
Nice plugin!
I have one question and a feature request.
Question. Is there a way to display extra details, such as ‘note’ or ‘abstract’?
Feature request. Can you enable different style formats (i.e., APA, MLA, Bluebook)?

Hello there;
Enhanced BibliPlug looked very promising to me, but after installation I find it difficult to use.

Documentation of the shortcodes is not linked from plugin settings or editing panel. one has to get the shortcodes from http://wordpress.org/extend/plugins/enhanced-bibliplug/
how does one keep track of reference ids / numbers? Listing page (“Bibliography” in Admin side nav > /wp-admin/edit.php?post_type=reference&page=enhanced-bibliplug/bibliplug_manager.php) does not list id# of references, which makes it difficult to use the shortcodes for single references.
Post editor doesn’t have a button (or at least none i could find) for easy insertion of references into post/s

Thanks for this plugin. I’m using it for listing books, a kind of bibliography, but without using all the famous things you’re providing (maybe later). The thing I can’t find is the way to display this bibilography feature on the blog itself for the common user, either as a new category or a link: is this possible or is this only a tool for professionnals and is only viewable as an administrator?

I have a problem wit authors: no matter how i try, i can’t add them to the db. I tried importing a ris file, synchronizing from zotero or adding manually. Nothing worked. It shows me the references (in the admin panel) correctly but without the author. When I add them manually, in the “Add new reference” page, filling the authors fields they simply disappear when I save changes. This plugin seems great, it would be a shame to not use it …

Thank you so much for such a great plugin! I have found it to be more useful than any other zotero plugin out there. However, I do have one question:

Within my online Zotero account, I have created hundreds of references that each have tags and categories applied to them. I need to be able to access that particular tag and category information within Wordpress. However, when I activated the plugin and linked it with my online Zotero account, the “Tags” and “Categories” options under the “Bibliographies” tab in the Dashboard sidebar did not populate with the tags and categories from my Zotero account. Is there anyway to incorporate this information? Have I done something wrong or am I looking in he wrong place? I am hoping to have this be automated so that I don’t have to re-tag all 300 references, and have that information be completely independent of Zotero. Any help would be greatly appreciated.

I have another request: a user marked as “editor” permissions can’t add references to the system. Do I really have to make all people I want to update the references administrators? Could you relax this, either down to Editor or lower, or simply give me a configuration option? I’d like all my students to be able to add references to our blog, but don’t want to make them all admins.

Hi, I’ve done some more poking at the code, and I’m stumped. I’m not a wordpress expert (I am technical, though) and it appears that you intended for non-admins to be able to edit, since you are using the wordpress capabilities to check things.

But, at least in my Network installation, it does not seem to work. If I set one to anything but Administrator or Network Administrator level (e.g., Editor), the can see the “Bibliography” entry in the dashboard, and the only submenus are “add new” and “all references” (ok, although I’d like them to be able to edit tags and/or categories too). But, if they try to add an entry, they get a permission error, and they don’t see anything listed in the “all references” list.

What a really nice plugin.
I wish to create a research filter by language and related area, but I’m not bringing off yet. What am I doing wrong? Concretely, I create some reference categories into the plugin menu. Then, I create some references indicating each time the related references. Finally, I create a menu with the reference categories. But when I click on each reference of the menu, I don’t found anything. The result is :
“Apologies, but no results were found for the requested archive. Perhaps searching will help find a related post”. Could you help me? There is a special code or a special procedure to create a menu research for this plugin?

I’m trying to use the ‘Import references in RIS format only’ function. It doesn’t work with the exported RIS – file created by Papers 2 (http://www.mekentosj.com/papers/). It states after uploading: Found a reference without title. Skipped. Number of references successfully imported: 0.
When I check the created ris-file by Papers, all info is there according to the RIS – format specifications.
Some advice is needed

This plugin works great for our bulletin board to inform my colleagues concerning medical articles.
The thing I miss is a ‘File ID’ in the bibliography overview. If I add an article from the bibliography in my post (like [bibliplug id = ##]), I have to figure out the ‘file ID’ manually. Can this be incorporated in plug in?
Thanks in advance for your reply

Hmm, that will be difficult. The only unique identifier for a reference is the ID, so that’s the only reliable way to show a single reference. A workaround would be to create a unique tag/category the particular reference you want to use. Then you can use [bibliplug tag='some human reable tag'] to avoid using the id.

Hi, I am thrilled to have found this plugin; it’s going to help us clean up the web pages for my research lab. A couple of requests/suggestions:
- I’d like to be able to enter the “doi” for each pub, which is a pretty standard digital link. Would let people go to the “source” for each pub. It would be nice if it showed up after the ref with a little icon or something (even just the word “DOI”) to let people know it’s that, and linked to http://www.doi.org/…thedoi….
- I really need to edit the categories! I think you mentioned that’s coming soon. In our computer science field, I have some different ones I want to put in.
- I would really like to be able to have some more structured attachments. For example, I’d like to attach the powerpoint slides, submitted video, and/or other materials to a conference reference. It would be nice if these showed up (as with DOI) as a small icon after the ref, with a link to the material (that is probably in my wordpress media library for the site)
- I create project pages for my projects in wordpress; it would be great if I could associate references with these projects. I am planning to do that right now via a hack (create a parallel set of categories to a page, and either hardcode the short code on the page itself, make a custom category on each page pointing to it’s bibliplug category, or make sure the slug of the page is the same as the bibliplug category). But, it would be cool if you could think of a way to automate that slightly (perhaps by allowing me to enter one or more “page” references with a citation, and then having a short code to show all refs related to a page).
- I’m not sure how this would work, but I’d love to be able to have a link on each reference in a list that either expanded to the full collection of information inline or jumped to a page showing it (e.g., showing abstract, note, etc). Perhaps that’s there and I’m just missing it.

Anyway, these are all minor things, but would be great to have. If you aren’t going to do them soon, we might hack them in; if we do, we’ll send you the patches, but if you are planning on any, I’d love to know it!

Thank you for your comment. Those are great ideas. I will definitely work on the DOI link and structured attachments. Bibliplug 1.3.0 is released and you can now edit categories and tags.

About associating a set of references to a page, I usually create a bibliplug category for that page, and just use the shortcode to show references in that category. I think this is similar to what you are doing already. A slight variation to this approach is to have custom templates for these pages so that some of manual work is done in the template. I generally try to avoid template approach as the installation is not straight forward and may not work with all themes, but your scenario is very interesting and I will definitely look into it more.

Wow, thanks for the fast update! I’ll try out the new features ASAP. We’re actively putting content into the system and trying to get the site up. I’m sure I’ll post new comments this week as I discover things.

I think your approach of categories is what we will do. It will give us some control.

One more suggestion: can there be a way to only print the “N most recent” in the plugin? On some old web pages, for each person we had up to 5 of each persons most recent publications listed. What I would like to do with your author page is list “Recent Publications” (up to 5) and “Recent Posts” (using wordpress post functionality).

Hi, thanks in advance for great work on this plugin. I’m currently evaluating it for use in our research group. But while I’ve successfully synced with a zotero account, only the [bibliplug id=n] shortcode seems to work for me, but none of the other options, such as last_name, year etc. Any ideas what could be up here?

Is there a way to make the short code tag more robust or is it limited by the class it’s extending? For example, I’d like to be able to retrieve 50 of the newest bibliographic entries arranged by the year they were published.

There seems to be no way to do that from here nor is there an easy way to do it in the plugin code that I can find.

I am using your great plug-in to build a bibliography and I have a page on my Web site to show all of them. So far so good. Now I am want to create a search botton to filter the list of references, any tips on that?

The search and the categories are the only things left to finnish my work.

Can you give me some more details on nhow you want to use the search button? For example, what shortcode do you use to show the references? Do you want the search to filter on all references or just the references shown on the page?

(I try to use Publication and Presentation but they did not work, no idea why)

Before I use your great plug-in I try WP-Table Reloaded, but this was really heavy. But something WP-TR has is a group of drop down list to filter the table in the page (post). I think this is made out of javascript. Possibly hiddening (do this word exist?) some DIV layers after selection.

I can’t get the bibliplug shortcode to work – I’ve tried uninstalling and reinstalling, different types of codes, etc. Other shortcodes (not from bibliplug) work fine. The Zotero connection syncs correctly, and I have all of the references listed correctly, but can’t get them into a post.

Unfortunately, the implementation I use for the rich text editor on the profile page is relying on a new feature/function in the upcoming WP 3.3, and is incompatible with 3.2.1. There have been lots of activity regarding to the_editor() function from 3.1 to 3.3, so making this feature back-compat is really hard, and the workarounds are simple too ugly to exist, so I have disabled this feature for WP version < 3.3.

WP 3.3 should be released next month, and the beta is avaliable to download right now.

Hi, I’ve just been playing around with this plugin and so far I think it’s awesome. It’s exactly the sort of system I was looking for! I’ve setup a zotero account, and I seem to have syncing working, but the sync is only working for the default “zotero quick start guide” and not any of the new articles I create in zotero. It is very strange. I imagine I’m possibly doing something wrong in the setup as I’m not familiar with this plugin or zotero, although can you think of anything obvious that I’ve done wrong. I’ve had an extensive fiddle and just can’t seem to work it out. Could I maybe mention that I look forward to the completion of this support page

I am happy to help, but need a little more information. Are your newly added references in a folder/collection in zotero? If so, can you try using the folder name in zotero as the collection name in the “zotero connector” page in wordpress? If not, can you send me a screen shot of your bibliplug “zotero connector” page, and some screen shots of your zotero settings? What messages do you get when you click “Sync” in the zotero connector? You can find my email address in the bibliplug.php file.

Hey guys,
I think your plugin is great and would like to use it for the knowledge management platform http://knowdoo.net that I’ve built.
But it seems like there is some kind of bug in the current version of the plugin when used in Wordpress 3.2.1
I tested it on different servers and with different browsers (Firefox, IE, Chrome) but if I try to add a new resource the input fields sometimes can’t be accessed and sometimes the submit buttons too.
Hope you can help me out with this

Yes, 1.2.8 fixed that bug with the categories and tags.
But with Firefox 7.0 and Opera 11.51 I still can’t edit the creator fields (first name, middle name, …). In Chrome 14 and Internet Explorer 8 all works fine.
And you have a typo in the “Add New” window, it says “Referece Tags”
Thanks!

Thanks!
What is still not working is the dropdown list “Type” for creators and details if I want to create a new reference. Either there is no dropdown list at all (Opera), one empty field (Firefox) or an empty list (IE).

Great. Many thanks for sorting so quickly. Seems to work now though still only does 50 at a time – message is “There are too many items in this connection that results are broken down to multiple pages. First 50 items are synchronized. To continue synchronize this connection, click the sync button again”.
Now, however, each pressing of “Sync” adds 50 more so got them all I think.
Not sure if I amend existing items in Zotero whether sync will therefore catch if Sync only looks at 50 at a time but will experiment and see.
Memory may be wrong but I don’t think when I deleted original I got a “Are you sure?” box. Given Sync and Delete buttons next to each other might be good to have that at some stage to prevent disaster striking.
Thanks again for the plug-in and quick updates from my queries. Look forward to experimenting with it as I develop the site over coming weeks.

Andrew – thanks for pushing on Bibliplug and helping us make it better! Upgrade to the just released version 1.2.3, and the error should be fixed (it worked on our test case with 450 Zotero references).

To start with a clean sync, delete your current Zotero connection and all associated references will be delated from the WordPress database (this will not change your references in Zotero). Then re-create it with the same Account ID and Private Key (go to WP Bibliography menu => Zotero Connector).

Thanks for update and answer to my email from Clifford. The update to 1.2.2 installed it still only input 50 items on first sync but this time when I followed advice and pressed “Sync” again, it added another 50 so it transferred 100 items (before it simply tried to sync the original 50 again). However, it now claims that there is no more to sync despite there being a lot more (perhaps too many as over 4,000 items?) in my Zotero account. Can you offer any further advice please?
Thanks,
Andrew.

1.2.2 was just released to fix two issues related to the Zotero Link: (1) Fixed bug for zotero sync when collection has more than 50 items and (2) changed the logic for syncing duplicate entries in zotero connectios, allowing the same reference linked to multiple collections.